#!/bin/bash
RUN_ID=SIMC012_AgFungi_Ribo
WORKING_DIR="/home/shichino/data/${RUN_ID}"

SAMPLE_LIST_A="pool_A.csv"
SAMPLE_LIST_B="pool_B.csv"
SAMPLE_LIST_C="pool_C.csv"
SAMPLE_LIST_D="pool_D.csv"

SAMPLE_ID_A=( $(cut -d ',' -f1 ${SAMPLE_LIST_A} ) )
SAMPLE_ID_B=( $(cut -d ',' -f1 ${SAMPLE_LIST_B} ) )
SAMPLE_ID_C=( $(cut -d ',' -f1 ${SAMPLE_LIST_C} ) )
SAMPLE_ID_D=( $(cut -d ',' -f1 ${SAMPLE_LIST_D} ) )

GENOMEINDEX_SOURCE="/home/genome/Colletotrichum_orbiculare/GCA_000350065.2/C.orbiculare_knownGene_STAR"
GENOMEINDEX_SOURCE_MITO="/home/genome/Colletotrichum_orbiculare/Mitochondria_Genome/C.orbiculare_knownGeneMITO_STAR"
DEPLETION_SOURCE="/home/genome/Colletotrichum_orbiculare/GCA_000350065.2/C.orbiculare_rtRNA_STAR"
GENE_SOURCE="/home/genome/Colletotrichum_orbiculare/5UTR_annotated/genes.txt"
GENE_SOURCE_MITO="/home/genome/Colletotrichum_orbiculare/Mitochondria_Genome/genes_mito.txt"
BED_SOURCE="/home/genome/Colletotrichum_orbiculare/5UTR_annotated/Cob_genes_with_UTRs.sort.1.bed"
BED_SOURCE_MITO="/home/genome/Colletotrichum_orbiculare/Mitochondria_Genome/Cob_mitochondrial.bed"

RAWFASTQ_SOURCE="${WORKING_DIR}/RawFastq/"

CLIPPED_OUT="${WORKING_DIR}/clipped"
SPLIT_OUT_A="${WORKING_DIR}/splitted_A"
SPLIT_OUT_B="${WORKING_DIR}/splitted_B"
SPLIT_OUT_C="${WORKING_DIR}/splitted_C"
SPLIT_OUT_D="${WORKING_DIR}/splitted_D"
UNALIGNED_OUT="${WORKING_DIR}/unaligned"
MAPPING_OUT="${WORKING_DIR}/mapped"
UNIQUE_READS_OUT="${WORKING_DIR}/unique"
FPFRAMING_OUT="${WORKING_DIR}/fpframing"
SHELL_IN_OUT="${WORKING_DIR}/shell_in_out"

ADAPTER_SEQ=AGATCGGAAGAGCACACGTCTGAA

PRE_SEQ=NN
POST_SEQ=NNNNNIIIII

echo "beginning riboscript"

mkdir ${CLIPPED_OUT} ${UNALIGNED_OUT} ${MAPPING_OUT} ${UNIQUE_READS_OUT} ${FPFRAMING_OUT} ${SHELL_IN_OUT}

echo "task: clipped reads"
date +"%Y/%m/%d %H:%M:%S"

echo "(nohup fastp -i ${RAWFASTQ_SOURCE}/SIMC012A_1.fastq.gz -I ${RAWFASTQ_SOURCE}/SIMC012A_2.fastq.gz -o ${CLIPPED_OUT}/SIMC012A_1_corrected.fastq -O ${CLIPPED_OUT}/SIMC012A_2_corrected.fastq --correction --disable_adapter_trimming --disable_quality_filtering -h ${CLIPPED_OUT}/SIMC012A_corrected.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh
echo "(nohup fastp -i ${CLIPPED_OUT}/SIMC012A_1_corrected.fastq -o ${CLIPPED_OUT}/SIMC012A_1_clipped.fastq -a ${ADAPTER_SEQ} --length_limit 149 -w 12 -h ${CLIPPED_OUT}/SIMC012A_clipped.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh

echo "(nohup fastp -i ${RAWFASTQ_SOURCE}/SIMC012B_1.fastq.gz -I ${RAWFASTQ_SOURCE}/SIMC012B_2.fastq.gz -o ${CLIPPED_OUT}/SIMC012B_1_corrected.fastq -O ${CLIPPED_OUT}/SIMC012B_2_corrected.fastq --correction --disable_adapter_trimming --disable_quality_filtering -h ${CLIPPED_OUT}/SIMC012B_corrected.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh
echo "(nohup fastp -i ${CLIPPED_OUT}/SIMC012B_1_corrected.fastq -o ${CLIPPED_OUT}/SIMC012B_1_clipped.fastq -a ${ADAPTER_SEQ} --length_limit 149 -w 12 -h ${CLIPPED_OUT}/SIMC012B_clipped.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh

echo "(nohup fastp -i ${RAWFASTQ_SOURCE}/SIMC012C_1.fastq.gz -I ${RAWFASTQ_SOURCE}/SIMC012C_2.fastq.gz -o ${CLIPPED_OUT}/SIMC012C_1_corrected.fastq -O ${CLIPPED_OUT}/SIMC012C_2_corrected.fastq --correction --disable_adapter_trimming --disable_quality_filtering -h ${CLIPPED_OUT}/SIMC012C_corrected.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh
echo "(nohup fastp -i ${CLIPPED_OUT}/SIMC012C_1_corrected.fastq -o ${CLIPPED_OUT}/SIMC012C_1_clipped.fastq -a ${ADAPTER_SEQ} --length_limit 149 -w 12 -h ${CLIPPED_OUT}/SIMC012C_clipped.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh

echo "(nohup fastp -i ${RAWFASTQ_SOURCE}/SIMC012D_1.fastq.gz -I ${RAWFASTQ_SOURCE}/SIMC012D_2.fastq.gz -o ${CLIPPED_OUT}/SIMC012D_1_corrected.fastq -O ${CLIPPED_OUT}/SIMC012D_2_corrected.fastq --correction --disable_adapter_trimming --disable_quality_filtering -h ${CLIPPED_OUT}/SIMC012D_corrected.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh
echo "(nohup fastp -i ${CLIPPED_OUT}/SIMC012D_1_corrected.fastq -o ${CLIPPED_OUT}/SIMC012D_1_clipped.fastq -a ${ADAPTER_SEQ} --length_limit 149 -w 12 -h ${CLIPPED_OUT}/SIMC012D_clipped.html) &" >> filtercommands.sh
echo "wait">> filtercommands.sh

source filtercommands.sh

# split by index
echo "task: split by index"
date +"%Y/%m/%d %H:%M:%S"

echo "(nohup fastx-split -o ${SPLIT_OUT_A} -p ${PRE_SEQ} -x ${POST_SEQ} --min-insert=10 -s ${SAMPLE_LIST_A} ${CLIPPED_OUT}/SIMC012A_1_clipped.fastq) &" >> splitcommands.sh
echo "(nohup fastx-split -o ${SPLIT_OUT_B} -p ${PRE_SEQ} -x ${POST_SEQ} --min-insert=10 -s ${SAMPLE_LIST_B} ${CLIPPED_OUT}/SIMC012B_1_clipped.fastq) &" >> splitcommands.sh
echo "(nohup fastx-split -o ${SPLIT_OUT_C} -p ${PRE_SEQ} -x ${POST_SEQ} --min-insert=10 -s ${SAMPLE_LIST_C} ${CLIPPED_OUT}/SIMC012C_1_clipped.fastq) &" >> splitcommands.sh
echo "(nohup fastx-split -o ${SPLIT_OUT_D} -p ${PRE_SEQ} -x ${POST_SEQ} --min-insert=10 -s ${SAMPLE_LIST_D} ${CLIPPED_OUT}/SIMC012D_1_clipped.fastq) &" >> splitcommands.sh

echo "wait" >> splitcommands.sh
source splitcommands.sh

# ncRNA depletion
echo "task: ncRNA depletion"
date +"%Y/%m/%d %H:%M:%S"
for id in ${SAMPLE_ID_A[@]}
do
		echo "(nohup mkdir ${UNALIGNED_OUT}/${id})" >> ncrnadepletioncommands.sh
        echo "(nohup STAR --genomeDir ${DEPLETION_SOURCE} --readFilesIn ${SPLIT_OUT_A}/${id}.fastq --runThreadN 12 --outFilterMultimapNmax 2000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${UNALIGNED_OUT}/${id}/ --alignIntronMax 1 --outReadsUnmapped Fastx --limitBAMsortRAM 10000000000) &" >> ncrnadepletioncommands.sh
		echo "wait">> ncrnadepletioncommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
		echo "(nohup mkdir ${UNALIGNED_OUT}/${id})" >> ncrnadepletioncommands.sh
        echo "(nohup STAR --genomeDir ${DEPLETION_SOURCE} --readFilesIn ${SPLIT_OUT_B}/${id}.fastq --runThreadN 12 --outFilterMultimapNmax 2000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${UNALIGNED_OUT}/${id}/ --alignIntronMax 1 --outReadsUnmapped Fastx --limitBAMsortRAM 10000000000) &" >> ncrnadepletioncommands.sh
		echo "wait">> ncrnadepletioncommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
		echo "(nohup mkdir ${UNALIGNED_OUT}/${id})" >> ncrnadepletioncommands.sh
        echo "(nohup STAR --genomeDir ${DEPLETION_SOURCE} --readFilesIn ${SPLIT_OUT_C}/${id}.fastq --runThreadN 12 --outFilterMultimapNmax 2000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${UNALIGNED_OUT}/${id}/ --alignIntronMax 1 --outReadsUnmapped Fastx --limitBAMsortRAM 10000000000) &" >> ncrnadepletioncommands.sh
		echo "wait">> ncrnadepletioncommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
		echo "(nohup mkdir ${UNALIGNED_OUT}/${id})" >> ncrnadepletioncommands.sh
        echo "(nohup STAR --genomeDir ${DEPLETION_SOURCE} --readFilesIn ${SPLIT_OUT_D}/${id}.fastq --runThreadN 12 --outFilterMultimapNmax 2000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${UNALIGNED_OUT}/${id}/ --alignIntronMax 1 --outReadsUnmapped Fastx --limitBAMsortRAM 10000000000) &" >> ncrnadepletioncommands.sh
		echo "wait">> ncrnadepletioncommands.sh
done
source ncrnadepletioncommands.sh


# Map rtRNA-depleted reads to fungus genome
echo "task: mapping"
date +"%Y/%m/%d %H:%M:%S"
for id in ${SAMPLE_ID_A[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/${id})" >> starcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/${id}/ --limitBAMsortRAM 10000000000) &" >> starcommands.sh
		echo "wait">> starcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/${id})" >> starcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/${id}/ --limitBAMsortRAM 10000000000) &" >> starcommands.sh
		echo "wait">> starcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/${id})" >> starcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/${id}/ --limitBAMsortRAM 10000000000) &" >> starcommands.sh
		echo "wait">> starcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/${id})" >> starcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/${id}/ --limitBAMsortRAM 10000000000) &" >> starcommands.sh
		echo "wait">> starcommands.sh
done

source starcommands.sh


# Map rRNA/tRNA depleted reads to mitochondria genome
echo "task: mitochondria-mapping"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/mito.${id})" >> mitostarcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE_MITO} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/mito.${id}/ --limitBAMsortRAM 10000000000) &" >> mitostarcommands.sh
		echo "wait">> mitostarcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/mito.${id})" >> mitostarcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE_MITO} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/mito.${id}/ --limitBAMsortRAM 10000000000) &" >> mitostarcommands.sh
		echo "wait">> mitostarcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/mito.${id})" >> mitostarcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE_MITO} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/mito.${id}/ --limitBAMsortRAM 10000000000) &" >> mitostarcommands.sh
		echo "wait">> mitostarcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
		echo "(nohup mkdir ${MAPPING_OUT}/mito.${id})" >> mitostarcommands.sh
        echo "(nohup STAR --genomeDir ${GENOMEINDEX_SOURCE_MITO} --readFilesIn ${UNALIGNED_OUT}/${id}/Unmapped.out.mate1 --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${MAPPING_OUT}/mito.${id}/ --limitBAMsortRAM 10000000000) &" >> mitostarcommands.sh
		echo "wait">> mitostarcommands.sh
done
source mitostarcommands.sh


#Extract mapped reads
echo "task: extract mapped reads"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
        echo "(nohup samtools view -b ${MAPPING_OUT}/${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/${id}.bam ) &" >> renamingcommands.sh
        echo "(nohup samtools view -b ${MAPPING_OUT}/mito.${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/mito.${id}.bam ) &" >> renamingcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
        echo "(nohup samtools view -b ${MAPPING_OUT}/${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/${id}.bam ) &" >> renamingcommands.sh
        echo "(nohup samtools view -b ${MAPPING_OUT}/mito.${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/mito.${id}.bam ) &" >> renamingcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
        echo "(nohup samtools view -b ${MAPPING_OUT}/${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/${id}.bam ) &" >> renamingcommands.sh
        echo "(nohup samtools view -b ${MAPPING_OUT}/mito.${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/mito.${id}.bam ) &" >> renamingcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
        echo "(nohup samtools view -b ${MAPPING_OUT}/${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/${id}.bam ) &" >> renamingcommands.sh
        echo "(nohup samtools view -b ${MAPPING_OUT}/mito.${id}/Aligned.sortedByCoord.out.bam > ${MAPPING_OUT}/mito.${id}.bam ) &" >> renamingcommands.sh
done

echo "wait">> renamingcommands.sh
source renamingcommands.sh


#Index bam files
echo "task: indexing bam file"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
	echo "(nohup samtools index ${MAPPING_OUT}/${id}.bam ) &" >> indexingcommands.sh
	echo "(nohup samtools index ${MAPPING_OUT}/mito.${id}.bam ) &" >> indexingcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
	echo "(nohup samtools index ${MAPPING_OUT}/${id}.bam ) &" >> indexingcommands.sh
	echo "(nohup samtools index ${MAPPING_OUT}/mito.${id}.bam ) &" >> indexingcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
	echo "(nohup samtools index ${MAPPING_OUT}/${id}.bam ) &" >> indexingcommands.sh
	echo "(nohup samtools index ${MAPPING_OUT}/mito.${id}.bam ) &" >> indexingcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
	echo "(nohup samtools index ${MAPPING_OUT}/${id}.bam ) &" >> indexingcommands.sh
	echo "(nohup samtools index ${MAPPING_OUT}/mito.${id}.bam ) &" >> indexingcommands.sh
done
echo "wait">>indexingcommands.sh
source indexingcommands.sh



#Suppress duplicated reads
echo "task: removing duplicates from bam file"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/${id}.bam -o ${UNIQUE_READS_OUT}/${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/mito.${id}.bam -o ${UNIQUE_READS_OUT}/mito.${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/mito.${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/${id}.bam -o ${UNIQUE_READS_OUT}/${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/mito.${id}.bam -o ${UNIQUE_READS_OUT}/mito.${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/mito.${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/${id}.bam -o ${UNIQUE_READS_OUT}/${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/mito.${id}.bam -o ${UNIQUE_READS_OUT}/mito.${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/mito.${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/${id}.bam -o ${UNIQUE_READS_OUT}/${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
        echo "(nohup bam-suppress-duplicates -i ${MAPPING_OUT}/mito.${id}.bam -o ${UNIQUE_READS_OUT}/mito.${id}_unique.bam --annotate --stats=${UNIQUE_READS_OUT}/mito.${id}_duplicate_stats.txt ) &" >> duplicatescommands.sh
done

echo "wait">>duplicatescommands.sh
source duplicatescommands.sh


#Index bam files
echo "task: re-indexing bam file"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> secondindexingcommands.sh
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> secondindexingcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> secondindexingcommands.sh
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> secondindexingcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> secondindexingcommands.sh
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> secondindexingcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> secondindexingcommands.sh
       echo "(nohup samtools index ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> secondindexingcommands.sh
done

echo "wait">>secondindexingcommands.sh
source secondindexingcommands.sh


#fp-framing
echo "task: fp-framing"
date +"%Y/%m/%d %H:%M:%S"

for id in ${SAMPLE_ID_A[@]}
do
       echo "(nohup fp-framing -l 15,35 --flanking=-300,300 -g ${GENE_SOURCE} -o ${FPFRAMING_OUT}/${id} -b ${BED_SOURCE} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh
       echo "(nohup fp-framing -l 15,40 -g ${GENE_SOURCE_MITO} -o ${FPFRAMING_OUT}/mito.${id} -b ${BED_SOURCE_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh

done

for id in ${SAMPLE_ID_B[@]}
do
       echo "(nohup fp-framing -l 15,35 --flanking=-300,300 -g ${GENE_SOURCE} -o ${FPFRAMING_OUT}/${id} -b ${BED_SOURCE} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh
       echo "(nohup fp-framing -l 15,40 -g ${GENE_SOURCE_MITO} -o ${FPFRAMING_OUT}/mito.${id} -b ${BED_SOURCE_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh

done

for id in ${SAMPLE_ID_C[@]}
do
       echo "(nohup fp-framing -l 15,35 --flanking=-300,300 -g ${GENE_SOURCE} -o ${FPFRAMING_OUT}/${id} -b ${BED_SOURCE} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh
       echo "(nohup fp-framing -l 15,40 -g ${GENE_SOURCE_MITO} -o ${FPFRAMING_OUT}/mito.${id} -b ${BED_SOURCE_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh

done

for id in ${SAMPLE_ID_D[@]}
do
       echo "(nohup fp-framing -l 15,35 --flanking=-300,300 -g ${GENE_SOURCE} -o ${FPFRAMING_OUT}/${id} -b ${BED_SOURCE} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh
       echo "(nohup fp-framing -l 15,40 -g ${GENE_SOURCE_MITO} -o ${FPFRAMING_OUT}/mito.${id} -b ${BED_SOURCE_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpframingcommands.sh
       echo "wait">>fpframingcommands.sh

done
source fpframingcommands.sh


cat filtercommands.sh >> list_of_commands_${RUN_ID}
cat splitcommands.sh >> list_of_commands_${RUN_ID}
cat ncrnadepletioncommands.sh >> list_of_commands_${RUN_ID}
cat starcommands.sh >> list_of_commands_${RUN_ID}
cat mitostarcommands.sh >> list_of_commands_${RUN_ID}
cat renamingcommands.sh >> list_of_commands_${RUN_ID}
cat indexingcommands.sh >> list_of_commands_${RUN_ID}
cat duplicatescommands.sh >> list_of_commands_${RUN_ID}
cat secondindexingcommands.sh >>  list_of_commands_${RUN_ID}
cat fpframingcommands.sh >>  list_of_commands_${RUN_ID}

rm *commands.sh
mv list_of_commands_${RUN_ID} ${SHELL_IN_OUT}

echo "exiting riboscript"
date +"%Y/%m/%d %H:%M:%S"

mv nohup.out ${SHELL_IN_OUT}